Project Proposal

Total Page:16

File Type:pdf, Size:1020Kb

Project Proposal Community Sequencing Program: Project Proposal Proposer’s Name: David HIBBETT, Dan CULLEN, Dan EASTWOOD, Francis MARTIN, Antonio PISABARRO, and Igor GRIGORIEV Project Title: Community proposal to sequence a diverse assemblage of saprotrophic Basidiomycota (Agaricomycotina) Proposal ID: A) Brief description: Abstract: We propose a community-based sequencing project for whole-genome sequencing of a suite of saprotrophic (decayer) Fungi in the Basidiomycota, subphylum Agaricomycotina. The proposed organisms are of central relevance to the DOE mission with regard to lignocellulose bioconversion, biofuel production, feedstock improvement, and carbon cycle functioning. This proposal is derived from the basidiomycete focus group of the JGI Fungal Genomics Program, which commenced in October 2009. The organisms targeted in this proposal are particularly relevant to the “Biorefinery” section of the Genomic Encyclopedia of Fungi that the FGP seeks to create. Scope of Work: We propose a suite of 30 species for genome sequencing, divided into two Tiers of 13 and 17 species each. This set of taxa includes all of the 24 saprotrophic species identified by the Basidiomycota community in response to the 2009 FGP. The Tier 1 taxa are already being processed as a “pilot project” of the FGP. We therefore propose the remaining seventeen species in Tier 2 for sequencing as a follow-up to the current pilot project. The taxa have been selected on the basis of five major criteria: 1) phylogenetic diversity, 2) functional diversity and ecological importance, 3) utility as experimental systems, and community interest, 4) complementarity and relevance to other CSP proposals, and 5) availability of starting materials (monokaryons) and experimental tractability. The chosen taxa represent fourteen of the approximately eighteen major clades (orders and subclasses) of Agaricomycotina, including five independent brown rot lineages. This selection has been developed in coordination with a parallel proposal by Francis Martin and colleagues to sequence the genomes of twenty-three ectomycorrhizal (ECM) taxa, including 18 Agaricomycotina and 5 Ascomycota. Together, the genomes of the saprotrophic taxa proposed here and the ECM taxa being proposed by Martin et al. will provide insight into the functional diversity of Agaricomycotina, including the genetic bases of transitions between saprotrophic and ECM lifestyles, as well as between white rot and brown rot. A third parallel proposal by Joseph Spatafora and colleagues proposes to sequence an assemblage of diverse Fungi representing undersampled branches of the fungal Tree of Life, with an emphasis on basal fungal lineages (the paraphyletic “chytrids” and “zygomycetes”). Several Basidiomycota are targeted in the Tree of Life proposal, but none are in the Agaricomycotina. The primary goals of the proposed genome sequencing effort are to describe gene content and facilitate functional (expression) and evolutionary analyses. It is understood that the sequencing technology is rapidly evolving. We therefore defer decisions regarding the optimal approach to WGS of these haploid monokaryons to the JGI staff. Illumina-based transcriptome analysis, specifically focused on colonized wood, is also being requested in this proposal. Augmenting the genome and transcriptome data, the PIs and collaborators will perform mass spectroscopy-based secretome analysis, wood compositional analysis and microscopy, all under standardized conditions. Finally, we will perform comparative phylogenetic analyses to assess the evolution of decay mechanisms in Agaricomycotina. B) Background information (Limit 3 pages) Technical Information: Direct information about genome size, G+C content, polymorphism level, and repeat structure is not available for the target taxa. Genomes for Agaricomycotina range from 19 Mbp in Cryptococcus neoformans (a pathogenic yeast in the Tremellomycetes) to 65 Mbp in Laccaria bicolor (an ectomycorrhizal mushroom in the Agaricales). The genome sizes for wood decay fungi have ranged from 35 Mbp (Phanerochaete chrysosporium, Polyporales) to 47 Mbp (Serpula lacrymans, Boletales). Based on comparisons with these fungi, the species proposed here are unlikely to have a problematic G+C content and the haploid genome sizes probably range from 30 to 50 Mb. Similarly, substantial amounts of repetitive DNA in the form of class I and II transposons and their remnants are expected. Up to 10% of the genome might be repetitive, although this is no longer particularly daunting for the JGI assembly team. (Another basidiomycete successfully sequenced by the JGI, Laccaria bicolor (Martin et al. 2008), was found to contain over 20% repeats and further complicated by a substantial amount of endobacterial DNA ‘contamination’.) Polymorphisms related to ploidy, which were problematic in the JGI Postia placenta genome project (Martinez et al. 2009), will be circumvented by sequencing monokaryons exclusively. Available Resources: Most of the taxa targeted here have not been used as model experimental systems, so there is little preliminary information about genome structure (e.g., physical maps, genetic maps, fingerprinted BAC libraries, etc). However, seven species (Bjerkandera adusta, Dichomitus squalens, Coniophora puteana, Fomitiporia mediterranea, Gloeophyllum trabeum, Phlebia brevispora, Trametes versicolor) have been used in various studies of decay chemistry, and there is published information on decay capabilities (e.g., ability to degrade crystalline cellulose by Gloeophyllum and Coniophora) and selected enzyme families (e.g., class II peroxidases and laccases in Bjerkandera adusta, Fomitiporia mediterranea, Phlebia brevispora, and Trametes versicolor) (Baldrian and Valaskova 2008, Lundell et al. 2010, Morgenstern et al. 2008). Genetic transformations systems are available for T. versicolor. Additionally, two species proposed here, Phanerochaete velutina and Phanerochaete flavido-alba, are closely related to the model white rot species Phanerochate chrysosporium, for which a complete genome sequence is available (Martinez et al. 2004). Technical Challenges: One of the Tier 2 target species, Hygrocybe sp., has yet to be successfully cultured on standard mycological media (e.g., malt-extract agar, potato-dextrose agar). We will attempt to obtain this organism as a monokaryotic culture using various enhanced media, such as Melins-Norkrans medium, vitamin-enhanced media, etc. Another Tier 2 target species, Sphaerobolus stellatus, is culturable, but attempts to obtain monokaryons have failed (it is possible that this species produces dikaryotic spores). We have identified several alternative taxa that are known to be culturable; Hydnomerulius pinastri or Marasmius spp. are alternatives for Hygrocybe sp., and Lentaria michneri is an alternative for Sphaerobolus stellatus. We will pursue monokaryotic cultures of the alternative taxa at the same time that we attempt to obtain monokaryotic cultures of Hygrocybe sp. and Sphaerobolus stellatus. Starting Materials: Saprotrophic Agaricomycotina are relatively easy to culture in both dikaryotic and monokaryotic forms and excellent culture collections exist in the United States and abroad. As noted, nucleic acids of thirteen monokaryotic strains have already been submitted and are in various stages of genome sequencing as a pilot project. Monokaryotic cultures for eight of the remaining 17 species have been located in the culture collections of the USDA Forest Products Laboratory (FPL), the University of Tennessee (TENN; laboratory of Ronald H. Petersen), and the Belgian Coordinated Collections of Microorganisms/Mycothèque de l'Universite catholique de Louvain (BCCM/MUCL; one species). Monokaryons of Phanerochaete velutina and Phanerochaete flavido-alba have not been located, but monokaryons of other closely related Phanerochaete species are present in FPL and could be substituted if necessary. Monokaryons of seven species will need to be located elsewhere or obtained from fruiting bodies collected from nature. Isolates in culture collections are occasionally misidentified. We will confirm identities of all cultures using sequences of the internal transcribed spacers (ITS1-2) of nuclear ribosomal genes. The PIs of the present proposal will obtain monokaryotic cultures of all of the target taxa from established culture collections and from new collections in nature, beginning in the summer of 2010. We anticipate that new DNA and RNA preparations will begin to be available for submission to JGI by the end of 2010. To aid annotation, we will continue to provide total RNA from various complex and defined media. For quantitative transcriptome analysis, total RNA and mRNA is isolated from wood using a system devised in Bob Blanchette’s laboratory (letter attached) (Vanden Wymelenberg et al. 2006). This method substantially reduces sample variation and involves thin wood wafers placed directly on actively growing mycelia. Wood wafers (1 cm X 1 cm X 2 mm) are cut from freshly harvested sapwood, sterilized and inoculated by contact with mycelium growing on malt extract agar (1.5% Difco malt extract and 1.5% agar liter-1) in Petri plates. Up to 100 ug high quality total RNA can be purified by simple modifications of the Qiagen RNEasy system. If Illumina transcriptome analysis is approved, mRNA may be preferred. If so, we can easily and efficiently purify mRNA from the colonized wafers by magnetic capture techniques. The wood-derived mRNA is an excellent template for cDNA synthesis. Ultimately, colonized
Recommended publications
  • The 2014 Golden Gate National Parks Bioblitz - Data Management and the Event Species List Achieving a Quality Dataset from a Large Scale Event
    National Park Service U.S. Department of the Interior Natural Resource Stewardship and Science The 2014 Golden Gate National Parks BioBlitz - Data Management and the Event Species List Achieving a Quality Dataset from a Large Scale Event Natural Resource Report NPS/GOGA/NRR—2016/1147 ON THIS PAGE Photograph of BioBlitz participants conducting data entry into iNaturalist. Photograph courtesy of the National Park Service. ON THE COVER Photograph of BioBlitz participants collecting aquatic species data in the Presidio of San Francisco. Photograph courtesy of National Park Service. The 2014 Golden Gate National Parks BioBlitz - Data Management and the Event Species List Achieving a Quality Dataset from a Large Scale Event Natural Resource Report NPS/GOGA/NRR—2016/1147 Elizabeth Edson1, Michelle O’Herron1, Alison Forrestel2, Daniel George3 1Golden Gate Parks Conservancy Building 201 Fort Mason San Francisco, CA 94129 2National Park Service. Golden Gate National Recreation Area Fort Cronkhite, Bldg. 1061 Sausalito, CA 94965 3National Park Service. San Francisco Bay Area Network Inventory & Monitoring Program Manager Fort Cronkhite, Bldg. 1063 Sausalito, CA 94965 March 2016 U.S. Department of the Interior National Park Service Natural Resource Stewardship and Science Fort Collins, Colorado The National Park Service, Natural Resource Stewardship and Science office in Fort Collins, Colorado, publishes a range of reports that address natural resource topics. These reports are of interest and applicability to a broad audience in the National Park Service and others in natural resource management, including scientists, conservation and environmental constituencies, and the public. The Natural Resource Report Series is used to disseminate comprehensive information and analysis about natural resources and related topics concerning lands managed by the National Park Service.
    [Show full text]
  • Genome Sequence Analysis of Auricularia Heimuer Combined with Genetic Linkage Map
    Journal of Fungi Article Genome Sequence Analysis of Auricularia heimuer Combined with Genetic Linkage Map Ming Fang 1, Xiaoe Wang 2, Ying Chen 2, Peng Wang 2, Lixin Lu 2, Jia Lu 2, Fangjie Yao 1,2,* and Youmin Zhang 1,* 1 Lab of genetic breeding of edible mushromm, Horticultural, College of Horticulture, Jilin Agricultural University, Changchun 130118, China; [email protected] 2 Engineering Research Centre of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun 130118, China; [email protected] (X.W.); [email protected] (Y.C.); [email protected] (P.W.); [email protected] (L.L.); [email protected] (J.L.) * Correspondence: [email protected] (F.Y.); [email protected] (Y.Z.) Received: 3 March 2020; Accepted: 12 March 2020; Published: 16 March 2020 Abstract: Auricularia heimuer is one of the most popular edible fungi in China. In this study, the whole genome of A. heimuer was sequenced on the Illumina HiSeq X system and compared with other mushrooms genomes. As a wood-rotting fungus, a total of 509 carbohydrate-active enzymes (CAZymes) were annotated in order to explore its potential capabilities on wood degradation. The glycoside hydrolases (GH) family genes in the A. heimuer genome were more abundant than the genes in the other 11 mushrooms genomes. The A. heimuer genome contained 102 genes encoding class III, IV, and V ethanol dehydrogenases. Evolutionary analysis based on 562 orthologous single-copy genes from 15 mushrooms showed that Auricularia formed an early independent branch of Agaricomycetes. The mating-type locus of A. heimuer was located on linkage group 8 by genetic linkage analysis.
    [Show full text]
  • Why Mushrooms Have Evolved to Be So Promiscuous: Insights from Evolutionary and Ecological Patterns
    fungal biology reviews 29 (2015) 167e178 journal homepage: www.elsevier.com/locate/fbr Review Why mushrooms have evolved to be so promiscuous: Insights from evolutionary and ecological patterns Timothy Y. JAMES* Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA article info abstract Article history: Agaricomycetes, the mushrooms, are considered to have a promiscuous mating system, Received 27 May 2015 because most populations have a large number of mating types. This diversity of mating Received in revised form types ensures a high outcrossing efficiency, the probability of encountering a compatible 17 October 2015 mate when mating at random, because nearly every homokaryotic genotype is compatible Accepted 23 October 2015 with every other. Here I summarize the data from mating type surveys and genetic analysis of mating type loci and ask what evolutionary and ecological factors have promoted pro- Keywords: miscuity. Outcrossing efficiency is equally high in both bipolar and tetrapolar species Genomic conflict with a median value of 0.967 in Agaricomycetes. The sessile nature of the homokaryotic Homeodomain mycelium coupled with frequent long distance dispersal could account for selection favor- Outbreeding potential ing a high outcrossing efficiency as opportunities for choosing mates may be minimal. Pheromone receptor Consistent with a role of mating type in mediating cytoplasmic-nuclear genomic conflict, Agaricomycetes have evolved away from a haploid yeast phase towards hyphal fusions that display reciprocal nuclear migration after mating rather than cytoplasmic fusion. Importantly, the evolution of this mating behavior is precisely timed with the onset of diversification of mating type alleles at the pheromone/receptor mating type loci that are known to control reciprocal nuclear migration during mating.
    [Show full text]
  • Appendix K. Survey and Manage Species Persistence Evaluation
    Appendix K. Survey and Manage Species Persistence Evaluation Establishment of the 95-foot wide construction corridor and TEWAs would likely remove individuals of H. caeruleus and modify microclimate conditions around individuals that are not removed. The removal of forests and host trees and disturbance to soil could negatively affect H. caeruleus in adjacent areas by removing its habitat, disturbing the roots of host trees, and affecting its mycorrhizal association with the trees, potentially affecting site persistence. Restored portions of the corridor and TEWAs would be dominated by early seral vegetation for approximately 30 years, which would result in long-term changes to habitat conditions. A 30-foot wide portion of the corridor would be maintained in low-growing vegetation for pipeline maintenance and would not provide habitat for the species during the life of the project. Hygrophorus caeruleus is not likely to persist at one of the sites in the project area because of the extent of impacts and the proximity of the recorded observation to the corridor. Hygrophorus caeruleus is likely to persist at the remaining three sites in the project area (MP 168.8 and MP 172.4 (north), and MP 172.5-172.7) because the majority of observations within the sites are more than 90 feet from the corridor, where direct effects are not anticipated and indirect effects are unlikely. The site at MP 168.8 is in a forested area on an east-facing slope, and a paved road occurs through the southeast part of the site. Four out of five observations are more than 90 feet southwest of the corridor and are not likely to be directly or indirectly affected by the PCGP Project based on the distance from the corridor, extent of forests surrounding the observations, and proximity to an existing open corridor (the road), indicating the species is likely resilient to edge- related effects at the site.
    [Show full text]
  • Major Clades of Agaricales: a Multilocus Phylogenetic Overview
    Mycologia, 98(6), 2006, pp. 982–995. # 2006 by The Mycological Society of America, Lawrence, KS 66044-8897 Major clades of Agaricales: a multilocus phylogenetic overview P. Brandon Matheny1 Duur K. Aanen Judd M. Curtis Laboratory of Genetics, Arboretumlaan 4, 6703 BD, Biology Department, Clark University, 950 Main Street, Wageningen, The Netherlands Worcester, Massachusetts, 01610 Matthew DeNitis Vale´rie Hofstetter 127 Harrington Way, Worcester, Massachusetts 01604 Department of Biology, Box 90338, Duke University, Durham, North Carolina 27708 Graciela M. Daniele Instituto Multidisciplinario de Biologı´a Vegetal, M. Catherine Aime CONICET-Universidad Nacional de Co´rdoba, Casilla USDA-ARS, Systematic Botany and Mycology de Correo 495, 5000 Co´rdoba, Argentina Laboratory, Room 304, Building 011A, 10300 Baltimore Avenue, Beltsville, Maryland 20705-2350 Dennis E. Desjardin Department of Biology, San Francisco State University, Jean-Marc Moncalvo San Francisco, California 94132 Centre for Biodiversity and Conservation Biology, Royal Ontario Museum and Department of Botany, University Bradley R. Kropp of Toronto, Toronto, Ontario, M5S 2C6 Canada Department of Biology, Utah State University, Logan, Utah 84322 Zai-Wei Ge Zhu-Liang Yang Lorelei L. Norvell Kunming Institute of Botany, Chinese Academy of Pacific Northwest Mycology Service, 6720 NW Skyline Sciences, Kunming 650204, P.R. China Boulevard, Portland, Oregon 97229-1309 Jason C. Slot Andrew Parker Biology Department, Clark University, 950 Main Street, 127 Raven Way, Metaline Falls, Washington 99153- Worcester, Massachusetts, 01609 9720 Joseph F. Ammirati Else C. Vellinga University of Washington, Biology Department, Box Department of Plant and Microbial Biology, 111 355325, Seattle, Washington 98195 Koshland Hall, University of California, Berkeley, California 94720-3102 Timothy J.
    [Show full text]
  • Distribution of Methionine Sulfoxide Reductases in Fungi and Conservation of the Free- 2 Methionine-R-Sulfoxide Reductase in Multicellular Eukaryotes
    bioRxiv preprint doi: https://doi.org/10.1101/2021.02.26.433065; this version posted February 27, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 1 Distribution of methionine sulfoxide reductases in fungi and conservation of the free- 2 methionine-R-sulfoxide reductase in multicellular eukaryotes 3 4 Hayat Hage1, Marie-Noëlle Rosso1, Lionel Tarrago1,* 5 6 From: 1Biodiversité et Biotechnologie Fongiques, UMR1163, INRAE, Aix Marseille Université, 7 Marseille, France. 8 *Correspondence: Lionel Tarrago ([email protected]) 9 10 Running title: Methionine sulfoxide reductases in fungi 11 12 Keywords: fungi, genome, horizontal gene transfer, methionine sulfoxide, methionine sulfoxide 13 reductase, protein oxidation, thiol oxidoreductase. 14 15 Highlights: 16 • Free and protein-bound methionine can be oxidized into methionine sulfoxide (MetO). 17 • Methionine sulfoxide reductases (Msr) reduce MetO in most organisms. 18 • Sequence characterization and phylogenomics revealed strong conservation of Msr in fungi. 19 • fRMsr is widely conserved in unicellular and multicellular fungi. 20 • Some msr genes were acquired from bacteria via horizontal gene transfers. 21 1 bioRxiv preprint doi: https://doi.org/10.1101/2021.02.26.433065; this version posted February 27, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license.
    [Show full text]
  • Hori Et Al 2013.Pdf
    Mycologia, 105(6), 2013, pp. 1412–1427. DOI: 10.3852/13-072 # 2013 by The Mycological Society of America, Lawrence, KS 66044-8897 Genomewide analysis of polysaccharides degrading enzymes in 11 white- and brown-rot Polyporales provides insight into mechanisms of wood decay Chiaki Hori cellulases belonging to families GH6, GH7, GH9 Department of Biomaterials Sciences, Graduate School of and carbohydrate-binding module family CBM1 are Agricultural and Life Sciences, University of Tokyo, l-l-l, lacking in genomes of brown-rot polyporales. In Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan, and Institute for Microbial and Biochemical Technology, addition, the presence of CDH and the expansion Forest Products Laboratory, 1 Gifford Pinchot Drive, of LPMO were observed only in white-rot genomes. Madison, Wisconsin 53726 Indeed, GH6, GH7, CDH and LPMO peptides were identified only in white-rot polypores. Genes encod- Jill Gaskell ing aldose 1-epimerase (ALE), previously detected Institute for Microbial and Biochemical Technology, Forest Products Laboratory, 1 Gifford Pinchot Drive, with CDH and cellulases in the culture filtrates, also Madison, Wisconsin 53726 were identified in white-rot genomes, suggesting a physiological connection between ALE, CDH, cellu- Kiyohiko Igarashi lase and possibly LPMO. For hemicellulose degrada- Masahiro Samejima tion, genes and peptides corresponding to GH74 Department of Biomaterials Sciences, Graduate School of Agricultural and Life Sciences, University of Tokyo, l-l-l, xyloglucanase, GH10 endo-xylanase, GH79 b-glucu- Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan ronidase, CE1 acetyl xylan esterase and CE15 glucur- onoyl methylesterase were significantly increased in David Hibbett white-rot genomes compared to brown-rot genomes.
    [Show full text]
  • Phylogenetic Classification of Trametes
    TAXON 60 (6) • December 2011: 1567–1583 Justo & Hibbett • Phylogenetic classification of Trametes SYSTEMATICS AND PHYLOGENY Phylogenetic classification of Trametes (Basidiomycota, Polyporales) based on a five-marker dataset Alfredo Justo & David S. Hibbett Clark University, Biology Department, 950 Main St., Worcester, Massachusetts 01610, U.S.A. Author for correspondence: Alfredo Justo, [email protected] Abstract: The phylogeny of Trametes and related genera was studied using molecular data from ribosomal markers (nLSU, ITS) and protein-coding genes (RPB1, RPB2, TEF1-alpha) and consequences for the taxonomy and nomenclature of this group were considered. Separate datasets with rDNA data only, single datasets for each of the protein-coding genes, and a combined five-marker dataset were analyzed. Molecular analyses recover a strongly supported trametoid clade that includes most of Trametes species (including the type T. suaveolens, the T. versicolor group, and mainly tropical species such as T. maxima and T. cubensis) together with species of Lenzites and Pycnoporus and Coriolopsis polyzona. Our data confirm the positions of Trametes cervina (= Trametopsis cervina) in the phlebioid clade and of Trametes trogii (= Coriolopsis trogii) outside the trametoid clade, closely related to Coriolopsis gallica. The genus Coriolopsis, as currently defined, is polyphyletic, with the type species as part of the trametoid clade and at least two additional lineages occurring in the core polyporoid clade. In view of these results the use of a single generic name (Trametes) for the trametoid clade is considered to be the best taxonomic and nomenclatural option as the morphological concept of Trametes would remain almost unchanged, few new nomenclatural combinations would be necessary, and the classification of additional species (i.e., not yet described and/or sampled for mo- lecular data) in Trametes based on morphological characters alone will still be possible.
    [Show full text]
  • Spelling out Jaapia Species
    View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Digital.CSIC Mycol Progress (2015) 14: 57 DOI 10.1007/s11557-015-1081-8 ORIGINAL ARTICLE Spelling out Jaapia species M. Teresa Telleria 1 & Margarita Dueñas1 & Ireneia Melo2 & Isabel Salcedo3 & María P. Martín1 Received: 23 March 2015 /Revised: 16 June 2015 /Accepted: 22 June 2015 /Published online: 9 July 2015 # German Mycological Society and Springer-Verlag Berlin Heidelberg 2015. This article is published with open access at Springerlink.com Abstract Jaapia is a wood-saprobic genus of corticioid fungi Keywords Basidiomycota . Agaricomycetes . Jaapiales . for which two species have been recognized: J. argillacea Corticioid fungi . Taxonomy . Barcoding . ITS . Bres. and J. ochroleuca (Bres.) Nannf. & J. Erikss. Whereas Morphological diagnostic characters the first one is easily recognized by its characteristic spores, the descriptions of the second indicated variable spores, which once led us to believe that J. ochroleuca could be a species Introduction complex rather than a single species. Eleven new ITS nrDNA sequences of J. ochroleuca were aligned with two obtained Jaapia was described by Bresadola (1911)toaccommodate from GenBank and four of J. argillacea. The molecular re- J. argillacea Bres., and for 20 years, this monotypic genus sults, parsimony analysis and KP2 distances clearly delimitate was accepted by several authors (von Höhnel 1912; Wakefield one highly supported Jaapia clade, with two subclades that and Pearson 1920; Bourdot and Galzin 1923, 1928; Rogers correspond to the two described species. Morphological stud- 1935). Nannfeldt and Eriksson (1953)consideredConiophora ies, including the holotype and isotype of J.
    [Show full text]
  • The Flora Mycologica Iberica Project Fungi Occurrence Dataset
    A peer-reviewed open-access journal MycoKeys 15: 59–72 (2016)The Flora Mycologica Iberica Project fungi occurrence dataset 59 doi: 10.3897/mycokeys.15.9765 DATA PAPER MycoKeys http://mycokeys.pensoft.net Launched to accelerate biodiversity research The Flora Mycologica Iberica Project fungi occurrence dataset Francisco Pando1, Margarita Dueñas1, Carlos Lado1, María Teresa Telleria1 1 Real Jardín Botánico-CSIC, Claudio Moyano 1, 28014, Madrid, Spain Corresponding author: Francisco Pando ([email protected]) Academic editor: C. Gueidan | Received 5 July 2016 | Accepted 25 August 2016 | Published 13 September 2016 Citation: Pando F, Dueñas M, Lado C, Telleria MT (2016) The Flora Mycologica Iberica Project fungi occurrence dataset. MycoKeys 15: 59–72. doi: 10.3897/mycokeys.15.9765 Resource citation: Pando F, Dueñas M, Lado C, Telleria MT (2016) Flora Mycologica Iberica Project fungi occurrence dataset. v1.18. Real Jardín Botánico (CSIC). Dataset/Occurrence. http://www.gbif.es/ipt/resource?r=floramicologicaiberi ca&v=1.18, http://doi.org/10.15468/sssx1e Abstract The dataset contains detailed distribution information on several fungal groups. The information has been revised, and in many times compiled, by expert mycologist(s) working on the monographs for the Flora Mycologica Iberica Project (FMI). Records comprise both collection and observational data, obtained from a variety of sources including field work, herbaria, and the literature. The dataset contains 59,235 records, of which 21,393 are georeferenced. These correspond to 2,445 species, grouped in 18 classes. The geographical scope of the dataset is Iberian Peninsula (Continental Portugal and Spain, and Andorra) and Balearic Islands. The complete dataset is available in Darwin Core Archive format via the Global Biodi- versity Information Facility (GBIF).
    [Show full text]
  • Fruiting Body Form, Not Nutritional Mode, Is the Major Driver of Diversification in Mushroom-Forming Fungi
    Fruiting body form, not nutritional mode, is the major driver of diversification in mushroom-forming fungi Marisol Sánchez-Garcíaa,b, Martin Rybergc, Faheema Kalsoom Khanc, Torda Vargad, László G. Nagyd, and David S. Hibbetta,1 aBiology Department, Clark University, Worcester, MA 01610; bUppsala Biocentre, Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, SE-75005 Uppsala, Sweden; cDepartment of Organismal Biology, Evolutionary Biology Centre, Uppsala University, 752 36 Uppsala, Sweden; and dSynthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Center, 6726 Szeged, Hungary Edited by David M. Hillis, The University of Texas at Austin, Austin, TX, and approved October 16, 2020 (received for review December 22, 2019) With ∼36,000 described species, Agaricomycetes are among the and the evolution of enclosed spore-bearing structures. It has most successful groups of Fungi. Agaricomycetes display great di- been hypothesized that the loss of ballistospory is irreversible versity in fruiting body forms and nutritional modes. Most have because it involves a complex suite of anatomical features gen- pileate-stipitate fruiting bodies (with a cap and stalk), but the erating a “surface tension catapult” (8, 11). The effect of gas- group also contains crust-like resupinate fungi, polypores, coral teroid fruiting body forms on diversification rates has been fungi, and gasteroid forms (e.g., puffballs and stinkhorns). Some assessed in Sclerodermatineae, Boletales, Phallomycetidae, and Agaricomycetes enter into ectomycorrhizal symbioses with plants, Lycoperdaceae, where it was found that lineages with this type of while others are decayers (saprotrophs) or pathogens. We constructed morphology have diversified at higher rates than nongasteroid a megaphylogeny of 8,400 species and used it to test the following lineages (12).
    [Show full text]
  • Type Studies in Polyporaceae 27. Species Described by P. Ch
    CZECH MYCOLOGY 64(1): 13–21, JULY 2, 2012 (ONLINE VERSION, ISSN 1805-1421) Type studies in Polyporaceae 27. Species described by P. Ch. Hennings LEIF RYVARDEN Biological Institute, University of Oslo, P.O. Box 1066, Blindern, N-0316 Oslo, Norway; [email protected] Ryvarden L. (2012): Type studies in Polyporaceae 27. Species described by P. Ch. Hennings. – Czech Mycol. 64(1): 13–21. 103 polypores described by P. Ch. Hennings have been examined based on the available types. Nine- teen species are accepted, 63 species are reduced to synonymy, the types of 19 species could not be found, while two names are illegitimate. Two new combinations are proposed: Tyromyces aquosus (Henn.) Ryvarden and Diplomitoporus daedaleiformis (Henn.) Ryvarden. These two species are provided with de- scriptions, while published recent descriptions are referred to for the other 17 accepted species. Key words: Polyporaceae, types, taxonomy, nomenclature, Berlin herbarium. Ryvarden L. (2012): Typové studie chorošů 27. Druhy popsané P. Ch. Henning- sem – Czech Mycol. 64(1): 13–21. Na základě studia dostupných typů bylo revidováno 103 druhů chorošů popsaných P. Ch. Henning- sem. 19 druhů je akceptováno, 63 zařazeno do synonymiky, typy 19 druhů nebyly nalezeny, jména 2 dru- hů jsou ilegitimní. Jsou publikovány dvě nové kombinace: Tyromyces aquosus (Henn.) Ryvarden a Di- plomitoporus daedaleiformis (Henn.) Ryvarden. Tyto dva druhy jsou podrobně popsány a u 17 dalších akceptovaných druhů jsou připojeny odkazy na již publikované revize. INTRODUCTION Paul Christoph Hennings (1841–1908) was a productive mycologist, who de- scribed besides other species 109 polypores, mostly from Africa and South Amer- ica.
    [Show full text]